As far as I can tell my problems were solved when I replaced the (replacement) cargo hatch struts. PO had installed a set that were an inch or two too short and it had the effect of pulling the top hatch piece of out of alignment. Agree with @Samppahj though - not ever gonna be a perfect fit.
Do the bolts operate to adjust the upper piece of the hatch or do you think the inner piece of the assembly has a floating piece that can shift (and thus the bolts should be tightened back down all the way)? I'll get the whole thing calibrated: the lock mechanism will catch / clock twice...